macOS header problem

[jennybc]

On Mojave, one often needs to make some missing headers available:

https://silvae86.github.io/sysadmin/mac/osx/mojave/beta/libxml2/2018/07/05/fixing-missing-headers-for-homebrew-in-mac-osx-mojave/

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Things are different on Catalina, for which the Mojave "fix" (the header-containing package) is not available. Summary courtesy of @kevinushey:

R 3.6.1-patched handles the issue by updating etc/Makeconf with:

CPPFLAGS = -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include

I think once could also fix the issue by putting that in their own ~/.R/Makevars file.
So I think the "do I have command line tools ready and installed?" checklist is now:

1. xcode-select --install (make sure command line tools are installed)
2. /usr/bin/git --version (may trigger the Xcode license agreement)
3. Update ~/.R/Makevars, or (on Mojave) install the header-providing package.

Also worth saying: if someone has Xcode installed, but not command line tools, then regular command line tools will still work, even though compilation may fail (since R expects to find and use command line tools explicitly, as opposed to the version that might be bundled with Xcode).
And Xcode bundles its own version of command line tools, and the system binaries are smart enough to find and use whichever one happens to be installed.

[jennybc]

More recent discovery by @kevinushey, shared in slack:

setting the environment variable

SDKROOT = /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

appears to be enough to fix compilation for older versions of R on macOS Catalina (without having to edit Makevars or Makeconf)
I think this is the moral equivalent of passing -isysroot <...>, which newer versions of R do